The number of hospitalized patients with a Clostridium difficile infection (CDI) discharge diagnosis has increased dramatically due in part to the use of more sensitive methods involving nucleic acid amplification for diagnosis and to the emergence of epidemic strains, such as BI/NAP1/027 and 078. Vancomycin and Metronidazole have long been preferred treatment options in CDI, but neither is fully effective as evidenced by up to 35% clinical recurrence and significant fatality rates. Medical treatment and hospitalization associated with CDI burdens the U.S. health care system with up to $3.8 billion in excess costs each year, with much of the expense attributable to disease recurrence. Reduction in recurrence, therefore, is a priority clinical need and major market opportunity.
There is a need in the art to provide a comprehensive categorization of individuals based on molecular and/or phenotypic variables in light of the complex genetic, proteomic, and environmental interactions associated with CDI. There is a need in the art to characterize molecules (such as nucleic acids) from the samples of individuals using biomarkers of clinical genotype, phenotype, activity, and/or treatment. Current FDA-approved diagnostic assays for CDI are limited by their cost, technical complexity, long assay duration and/or sensitivity. No diagnostic assays currently exist that predict disease relapse in CDI, and these are urgently warranted, nor are there available any treatment therapies based on such diagnostic information.